GOTM as a host for interstitial water / sea-floor / sediment?

[platipodium]

I am aware that GOTM is all about turbulence and so running it in a non-turbulent environment, like in interstitial water within a sediment might miss its strength. But could still provide its rich infrastructure (flexout, fabm, B.C) !!

Let me still ask: is it possible to parameterise GOTM such that it runs in interstitial water?

This would probably require adding some information on porosity (possibly as a profile, or get around this with some other hack) and it would mean to reduce turbulence and diffusivity a lot.

But maybe this is a stupid idea?

[lumlauf]

Hi Carsten, Are you aware that we recently extended GOTM to include a vertically resolved sediment module in GOTM (see https://doi.org/10.1029/2023JC019651 <https://doi.org/10.1029/2023JC019651>)? At the moment, benthic transports are exclusively diffusive (cohesive sediments). But we are working on an extension towards non-cohesive sediments with advective fluxes, driven by surface-wave effects. Is this what you mean when talking about interstitial water?

…

-Lars

On 12/17/2025 9:26 AM, Carsten Lemmen wrote: I am aware that GOTM is all about turbulence and so running it in a non-turbulent environment, like in interstitial water within a sediment might miss its strength. But could still provide its rich infrastructure (flexout, fabm, B.C) !! Let me still ask: is it possible to parameterise GOTM such that it runs in interstitial water? This would probably require adding some information on porosity (possibly as a profile, or get around this with some other hack) and it would mean to reduce turbulence and diffusivity a lot. But maybe this is a stupid idea? — Reply to this email directly, view it on GitHub <#80>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEVOCRO22Q5UPBJ6LBNZYJL4CEHSVAVCNFSM6AAAAACPJDQKBOVHI2DSMVQWIX3LMV43ERDJONRXK43TNFXW4OZZGI2TKNRXGU>. You are receiving this because you are subscribed to this thread.Web Bug from https://github.com/notifications/beacon/AEVOCRLSMSOG4DIGPX4B2ZT4CEHSVA5CNFSM6AAAAACPJDQKBOWGG33NNVSW45C7OR4XAZNKIRUXGY3VONZWS33OVJRW63LNMVXHIX3JMTHABDJ27M.gifMessage ID: ***@***.***> ; [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "#80", "url": "#80", "name": "View Discussion" }, "description": "View this Discussion on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

-- ------------------------------------------------ Lars Umlauf Department of Physical Oceanography Leibniz-Institute for Baltic Sea Research phone : ++49 381 5197 223 fax : ++49 381 5197 114 web :www.io-warnemuende.de/lars-umlauf-en.html address: Leibniz-Institute for Baltic Sea Research Seestrasse 15 D-18119 Rostock-Warnemuende Germany -------------------------------------------------

[platipodium]

HI Lars, this is exactly what I was looking for! And no, I was not aware of the publication, thanks for pointing me to it. I'll try to replicate the work with the setups claimed to be published on Zenodo... anything else I need to be aware of?

Thanks,
Carsten

[lumlauf]

Hi Carsten, We actually have an improved, more recent version of this code, which has been carefully tested and is also now based on the most recent version of FABM. I'll send you a separate email with all the relevant people in CC in a minute. Cheers, Lars

…

On 12/17/2025 6:17 PM, Carsten Lemmen wrote: HI Lars, this is /exactly/ what I was looking for! And no, I was not aware of the publication, thanks for pointing me to it. I'll try to replicate the work with the setups claimed to be published on Zenodo... anything else I need to be aware of? Thanks, Carsten — Reply to this email directly, view it on GitHub <#80 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEVOCRO26L4Y5GEOCUJTA5L4CGFZHAVCNFSM6AAAAACPJDQKBOVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTKMRYGE3TCMI>. You are receiving this because you commented.Web Bug from https://github.com/notifications/beacon/AEVOCRPRAAQXA3TDRYKT5O34CGFZHA5CNFSM6AAAAACPJDQKBOWGG33NNVSW45C7OR4XAZNRIRUXGY3VONZWS33OINXW23LFNZ2KUY3PNVWWK3TUL5UWJTQA5EXC6.gifMessage ID: ***@***.***> [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "#80 (reply in thread)","url": "#80 (reply in thread)", "name": "View Discussion" }, "description": "View this Discussion on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

-- ------------------------------------------------ Lars Umlauf Department of Physical Oceanography Leibniz-Institute for Baltic Sea Research phone : ++49 381 5197 223 fax : ++49 381 5197 114 web :www.io-warnemuende.de/lars-umlauf-en.html address: Leibniz-Institute for Baltic Sea Research Seestrasse 15 D-18119 Rostock-Warnemuende Germany -------------------------------------------------

[bolding]

Is it an FABM only thing - or changes to GOTM as well?

[lumlauf]

As far as I understand, only/mainly the interface to FABM has been modified. Strongly modified as it now also includes the grid, variables, and time stepping for the vertically resolved sediment compartment. But Knut would be the better person to comment on this. He has implemented it. Lars

…

On 12/17/2025 7:25 PM, Karsten Bolding wrote: Is it an FABM only thing - or changes to GOTM as well? — Reply to this email directly, view it on GitHub <#80 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEVOCRI2YVLESVBD2XMCAET4CGN2JAVCNFSM6AAAAACPJDQKBOVHI2DSMVQWIX3LMV43URDJONRXK43TNFXW4Q3PNVWWK3TUHMYTKMRYGIZDCMI>. You are receiving this because you commented.Web Bug from https://github.com/notifications/beacon/AEVOCRMNBG36JQBVIX53RVD4CGN2JA5CNFSM6AAAAACPJDQKBOWGG33NNVSW45C7OR4XAZNRIRUXGY3VONZWS33OINXW23LFNZ2KUY3PNVWWK3TUL5UWJTQA5EYCG.gifMessage ID: ***@***.***> [ { ***@***.***": "http://schema.org", ***@***.***": "EmailMessage", "potentialAction": { ***@***.***": "ViewAction", "target": "#80 (comment)","url": "#80 (comment)", "name": "View Discussion" }, "description": "View this Discussion on GitHub", "publisher": { ***@***.***": "Organization", "name": "GitHub", "url": "https://github.com" } } ]

-- ------------------------------------------------ Lars Umlauf Department of Physical Oceanography Leibniz-Institute for Baltic Sea Research phone : ++49 381 5197 223 fax : ++49 381 5197 114 web :www.io-warnemuende.de/lars-umlauf-en.html address: Leibniz-Institute for Baltic Sea Research Seestrasse 15 D-18119 Rostock-Warnemuende Germany -------------------------------------------------